Module: Labimotion::ElementHelpers

Extended by:
Grape::API::Helpers
Defined in:
lib/labimotion/helpers/element_helpers.rb

Overview

ElementHelpers

Instance Method Summary collapse

Instance Method Details

#create_element(current_user, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 66

def create_element(current_user, params)
  klass = params[:element_klass] || {}
  uuid = SecureRandom.uuid
  params[:properties]['uuid'] = uuid
  params[:properties]['klass_uuid'] = klass[:uuid]
  params[:properties]['eln'] = Chemotion::Application.config.version
  params[:properties]['labimotion'] = Labimotion::VERSION
  params[:properties]['klass'] = 'Element'
  properties = params[:properties]
  properties.delete('flow') unless properties['flow'].nil?
  properties.delete('select_options') unless properties['select_options'].nil?
  attributes = {
    name: params[:name],
    element_klass_id: klass[:id],
    uuid: uuid,
    klass_uuid: klass[:uuid],
    properties: properties,
    properties_release: params[:properties_release],
    created_by: current_user.id,
  }
  element = Labimotion::Element.new(attributes)

  if params[:collection_id]
    collection = current_user.collections.find(params[:collection_id])
    element.collections << collection
  end
  all_coll = Collection.get_all_collection_for_user(current_user.id)
  element.collections << all_coll
  element.save!
  element.properties = update_sample_association(element, params[:properties], current_user)
  element.container = update_datamodel(params[:container], current_user)
  element.save!
  element.save_segments(segments: params[:segments], current_user_id: current_user.id)
  element
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#create_element_klass(current_user, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 19

def create_element_klass(current_user, params)
  uuid = SecureRandom.uuid
  template = { uuid: uuid, layers: {}, select_options: {} }
  attributes = declared(params, include_missing: false)
  attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
  attributes[:properties_template] = template unless attributes[:properties_template].present?
  attributes[:properties_template]['eln'] = Chemotion::Application.config.version if attributes[:properties_template].present?
  attributes[:properties_template]['labimotion'] = Labimotion::VERSION if attributes[:properties_template].present?
  attributes[:properties_template]['klass'] = 'ElementKlass' if attributes[:properties_template].present?
  attributes[:is_active] = false
  attributes[:uuid] = uuid
  attributes[:released_at] = DateTime.now
  attributes[:properties_release] = attributes[:properties_template]
  attributes[:created_by] = current_user.id

  new_klass = Labimotion::ElementKlass.create!(attributes)
  new_klass.reload
  new_klass.create_klasses_revision(current_user.id)
  klass_names_file = Rails.root.join('config', 'klasses.json')
  klasses = Labimotion::ElementKlass.where(is_active: true)&.pluck(:name) || []
  File.write(klass_names_file, klasses)
  klasses
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#element_revisions(params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 181

def element_revisions(params)
  klass = Labimotion::Element.find(params[:id])
  list = klass.elements_revisions unless klass.nil?
  list&.sort_by(&:created_at)&.reverse
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#klass_list(is_generic_only) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 11

def klass_list(is_generic_only)
  if is_generic_only == true
    Labimotion::ElementKlass.where(is_active: true, is_generic: true).order('place') || []
  else
    Labimotion::ElementKlass.where(is_active: true).order('place') || []
  end
end

#list_serialized_elements(params, current_user) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 230

def list_serialized_elements(params, current_user)
  collection_id =
  if params[:collection_id]
    Collection
      .belongs_to_or_shared_by(current_user.id, current_user.group_ids)
      .find_by(id: params[:collection_id])&.id
  elsif params[:sync_collection_id]
    current_user
      .all_sync_in_collections_users
      .find_by(id: params[:sync_collection_id])&.collection&.id
  end

  scope =
  if collection_id
    Labimotion::Element
      .joins(:element_klass, :collections_elements)
      .where(
        element_klasses: { name: params[:el_type] },
        collections_elements: { collection_id: collection_id },
      ).includes(:tag, collections: :sync_collections_users).order('created_at DESC')
  else
    Labimotion::Element.none
  end

  ## TO DO: refactor labimotion
  from = params[:from_date]
  to = params[:to_date]
  by_created_at = params[:filter_created_at] || false
  scope = scope.created_time_from(Time.at(from)) if from && by_created_at
  scope = scope.created_time_to(Time.at(to) + 1.day) if to && by_created_at
  scope = scope.updated_time_from(Time.at(from)) if from && !by_created_at
  scope = scope.updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
  scope
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#list_user_elements(scope, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 190

def list_user_elements(scope, params)
  from = params[:from_date]
  to = params[:to_date]
  by_created_at = params[:filter_created_at] || false

  if params[:sort_column]&.include?('.')
    layer, field = params[:sort_column].split('.')

    element_klass = Labimotion::ElementKlass.find_by(name: params[:el_type])
    allowed_fields = element_klass.properties_release.dig('layers', layer, 'fields')&.pluck('field') || []

    if field.in?(allowed_fields)
      query = ActiveRecord::Base.sanitize_sql(
        [
          "LEFT JOIN LATERAL(
            SELECT field->'value' AS value
            FROM jsonb_array_elements(properties->'layers'->:layer->'fields') a(field)
            WHERE field->>'field' = :field
          ) a ON true",
          { layer: layer, field: field },
        ],
      )
      scope = scope.joins(query).order('value ASC NULLS FIRST')
    else
      scope = scope.order(updated_at: :desc)
    end
  else
    scope = scope.order(updated_at: :desc)
  end

  scope = scope.created_time_from(Time.at(from)) if from && by_created_at
  scope = scope.created_time_to(Time.at(to) + 1.day) if to && by_created_at
  scope = scope.updated_time_from(Time.at(from)) if from && !by_created_at
  scope = scope.updated_time_to(Time.at(to) + 1.day) if to && !by_created_at
  scope
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#update_element_by_id(current_user, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 105

def update_element_by_id(current_user, params)
  element = Labimotion::Element.find(params[:id])
  update_datamodel(params[:container], current_user)
  properties = update_sample_association(element, params[:properties], current_user)
  params.delete(:container)
  params.delete(:properties)
  attributes = declared(params.except(:segments), include_missing: false)
  properties['eln'] = Chemotion::Application.config.version
  properties['labimotion'] = Labimotion::VERSION
  if element.klass_uuid != properties['klass_uuid'] || element.properties != properties || element.name != params[:name]
    properties['klass'] = 'Element'
    uuid = SecureRandom.uuid
    properties['uuid'] = uuid

    properties.delete('flow') unless properties['flow'].nil?
    properties.delete('select_options') unless properties['select_options'].nil?

    attributes['properties'] = properties
    attributes['properties']['uuid'] = uuid
    attributes['uuid'] = uuid
    attributes['klass_uuid'] = properties['klass_uuid']

    element.update(attributes)
  end
  element.save_segments(segments: params[:segments], current_user_id: current_user.id)
  element
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#update_element_klass(current_user, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 46

def update_element_klass(current_user, params)
  place = params[:place] || 100
  begin
    place = place.to_i if place.present? && place.to_i == place.to_f
  rescue StandardError
    place = 100
  end
  klass = Labimotion::ElementKlass.find(params[:id])
  klass.label = params[:label] if params[:label].present?
  klass.klass_prefix = params[:klass_prefix] if params[:klass_prefix].present?
  klass.icon_name = params[:icon_name] if params[:icon_name].present?
  klass.desc = params[:desc] if params[:desc].present?
  klass.place = place
  klass.save!
  klass
rescue => e
  Labimotion.log_exception(e, current_user)
  raise e
end

#upload_generics_files(current_user, params) ⇒ Object 



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# File 'lib/labimotion/helpers/element_helpers.rb', line 136

def upload_generics_files(current_user, params)
  attach_ary = []
  att_ary = create_uploads(
    'Element',
    params[:att_id],
    params[:elfiles],
    params[:elInfo],
    current_user.id,
  ) if params[:elfiles].present? && params[:elInfo].present?

  (attach_ary << att_ary).flatten! unless att_ary&.empty?

  att_ary = create_uploads(
    'Segment',
    params[:att_id],
    params[:sefiles],
    params[:seInfo],
    current_user.id
  ) if params[:sefiles].present? && params[:seInfo].present?

  (attach_ary << att_ary).flatten! unless att_ary&.empty?

  if params[:attfiles].present? || params[:delfiles].present? then
    att_ary = create_attachments(
      params[:attfiles],
      params[:delfiles],
      params[:att_type],
      params[:att_id],
      params[:attfilesIdentifier],
      current_user.id
    )
  end
  (attach_ary << att_ary).flatten! unless att_ary&.empty?

  if Labimotion::IS_RAILS5 == true
    TransferThumbnailToPublicJob.set(queue: "transfer_thumbnail_to_public_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
    TransferFileFromTmpJob.set(queue: "transfer_file_from_tmp_#{current_user.id}").perform_now(attach_ary) unless attach_ary.empty?
  end
  true
rescue => e
  Labimotion.log_exception(e, current_user)
  ## false
  raise e
end